library(skimr)
library(openxlsx)
library(ggrepel)
library(dplyr)
library(tidyr)
library(data.table)
library(broom)
library(broomExtra)
library(tibble)
library(sjstats)
library(car)
library(lme4)
library(lmerTest)
library(ggplot2)
library(tibble)
library(modelr)
library(tidyverse)
#library(miceadds)
library(ggforce)
require(openxlsx)
library(tidyverse)
library(caret)
library(glmnet)
library(ggplot2)
library(gridExtra)
library(MASS) # rlm
library(lmPerm)
library(circlize)
library(RColorBrewer)
library(ComplexHeatmap)
select <- dplyr::select
filter <- dplyr::filter
dir.IlluminaProductFiles <- "/Users/shawjes/Dropbox/EspinosaGroup/DATA_MAIN/MEGA/chr21_genotyping/Illumina_ProductFiles"
dir.chr21_genotyping <- "/Users/shawjes/Dropbox/EspinosaGroup/DATA_MAIN/MEGA/chr21_genotyping"
dir.chr21_idatQuants <- "/Users/shawjes/Dropbox/EspinosaGroup/DATA_MAIN/MEGA/chr21_genotyping/idatQuants"
dir.GRSdata <- "/Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Data"
dir.GRSplots <- "/Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Plots"
dir.GRSoriginal.Anno <- "/Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Annotation/GRSoriginal"
dir.GRSrevised.Anno <- "/Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Annotation/GRSrevised"
dir.PCA <- '/Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Data/PCA'
dir.Results <- '/Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Results'
save.sessionInfo <- sessionInfo()
save.sessionInfo
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] glmnet_4.1-3 lmerTest_3.1-3 lme4_1.1-29 Matrix_1.4-1 ComplexHeatmap_2.8.0 RColorBrewer_1.1-3 circlize_0.4.14
[8] lmPerm_2.1.0 MASS_7.3-56 gridExtra_2.3 caret_6.0-91 lattice_0.20-45 ggforce_0.3.3 modelr_0.1.8
[15] car_3.0-12 carData_3.0-5 sjstats_0.18.1 broomExtra_4.3.2 broom_0.7.12 ggrepel_0.9.1 openxlsx_4.2.5
[22] skimr_2.1.3 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
[29] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1 data.table_1.14.2
loaded via a namespace (and not attached):
[1] readxl_1.4.0 backports_1.4.1 plyr_1.8.7 repr_1.1.4 splines_4.1.1 listenv_0.8.0 TH.data_1.1-0
[8] digest_0.6.29 foreach_1.5.2 htmltools_0.5.2 fansi_1.0.3 magrittr_2.0.3 cluster_2.1.3 doParallel_1.0.17
[15] tzdb_0.3.0 recipes_0.2.0 globals_0.14.0 gower_1.0.0 matrixStats_0.61.0 sandwich_3.0-1 hardhat_0.2.0
[22] colorspace_2.0-3 rvest_1.0.2 haven_2.4.3 xfun_0.30 crayon_1.5.1 jsonlite_1.8.0 survival_3.3-1
[29] zoo_1.8-9 iterators_1.0.14 glue_1.6.2 polyclip_1.10-0 gtable_0.3.0 ipred_0.9-12 emmeans_1.7.3
[36] GetoptLong_1.0.5 sjmisc_2.8.9 shape_1.4.6 future.apply_1.8.1 BiocGenerics_0.38.0 abind_1.4-5 scales_1.2.0
[43] mvtnorm_1.1-3 DBI_1.1.2 Rcpp_1.0.8.3 xtable_1.8-4 performance_0.9.0 clue_0.3-60 stats4_4.1.1
[50] lava_1.6.10 prodlim_2019.11.13 datawizard_0.4.0 httr_1.4.2 ellipsis_0.3.2 pkgconfig_2.0.3 farver_2.1.0
[57] nnet_7.3-17 sass_0.4.1 dbplyr_2.1.1 utf8_1.2.2 tidyselect_1.1.2 rlang_1.0.2 reshape2_1.4.4
[64] effectsize_0.6.0.1 munsell_0.5.0 cellranger_1.1.0 tools_4.1.1 cli_3.2.0 generics_0.1.2 sjlabelled_1.1.8
[71] evaluate_0.15 fastmap_1.1.0 yaml_2.3.5 ModelMetrics_1.2.2.2 knitr_1.38 fs_1.5.2 zip_2.2.0
[78] future_1.24.0 nlme_3.1-157 xml2_1.3.3 compiler_4.1.1 rstudioapi_0.13 png_0.1-7 reprex_2.0.1
[85] tweenr_1.0.2 bslib_0.3.1 stringi_1.7.6 parameters_0.17.0 nloptr_2.0.0 vctrs_0.4.0 pillar_1.7.0
[92] lifecycle_1.0.1 jquerylib_0.1.4 GlobalOptions_0.1.2 estimability_1.3 insight_0.17.0 R6_2.5.1 IRanges_2.26.0
[99] parallelly_1.30.0 codetools_0.2-18 boot_1.3-28 assertthat_0.2.1 rjson_0.2.21 withr_2.5.0 S4Vectors_0.30.2
[106] multcomp_1.4-18 bayestestR_0.11.5 parallel_4.1.1 hms_1.1.1 rpart_4.1.16 timeDate_3043.102 coda_0.19-4
[113] class_7.3-20 minqa_1.2.4 rmarkdown_2.13 Cairo_1.5-15 pROC_1.18.0 numDeriv_2016.8-1.1 lubridate_1.8.0
[120] base64enc_0.1-3
theme_set(theme_gray(base_size = 12, base_family = "Arial") +
theme(panel.border = element_rect(colour="black", fill = "transparent"),
plot.title = element_text(face="bold", hjust = 0), # lineheight=.8, size=20,
axis.text = element_text(color="black", size = 14),
axis.text.x = element_text(angle = 0, hjust = NULL),
strip.background = element_rect(colour="black", fill = "light grey", size = 1), # adjusts facet label borders (if any)
panel.background = element_blank(),
panel.grid = element_blank()
))
RedBlue <- c("#CD3333", "#1874CD")
GrayBlue <- c("grey", "#2b8cbe")
ID_colnames <- c("FamilyID", "RecordID", "MEGA.FID", "MEGA.IID", "MEGA.LabID")
setwd(dir.GRSdata)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Data inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
analysis_meta <- fread("MEGA_041822_META_CeliacGRS_v0.1_JRS.csv") %>%
select(ID_colnames, Celiac, LabID, Celiac, EXCLUDE_from_analysis, EXCLUDE_reason) %>%
unique()
Note: Using an external vector in selections is ambiguous.
ℹ Use `all_of(ID_colnames)` instead of `ID_colnames` to silence this message.
ℹ See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
This message is displayed once per session.
analysis_meta
setwd(dir.GRSdata)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Data inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
analysisData.GRSorig <- fread("MEGA_041822_AnalysisData_CDGRS_Sharp2019_v0.1_JRS.csv") %>%
left_join(analysis_meta, by = ID_colnames) %>%
filter(EXCLUDE_from_analysis == 0)
analysisData.GRSrevised <- fread("MEGA_041822_AnalysisData_CDGRS_Sharp2022_v0.1_JRS.csv") %>%
left_join(analysis_meta, by = ID_colnames) %>%
filter(EXCLUDE_from_analysis == 0)
analysisData.GRSorig
analysisData.GRSrevised
analysisData.GRSorig %>% nrow()
[1] 9996
(analysisData.GRSorig %>% select(`Variant (Sharp 2019)`) %>% unique() %>% nrow())*(analysisData.GRSorig %>% select(RecordID) %>% unique() %>% nrow())
[1] 9996
analysisData.GRSrevised %>% nrow()
[1] 9996
(analysisData.GRSrevised %>% select(`Variant (Sharp 2022)`) %>% unique() %>% nrow())*(analysisData.GRSrevised %>% select(RecordID) %>% unique() %>% nrow())
[1] 9996
setwd(dir.PCA)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Data/PCA inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
ancestry_PCs <- fread("MEGA_041822_Espinosa_MEGA2_HTP_GS_08132019_updated_callrate_passing_QC_KEEPforHLAvsCeliac_EXCLUDEvariants_mind05_geno0.02_maf0.05_PRUNEDindeppairwise0.2_v0.1_JRS.eigenvec") %>%
select(FID, IID, PC1, PC2, PC3, PC4, PC5) %>%
rename(MEGA.FID = FID, MEGA.IID = IID)
ancestry_PCs
analysisData.GRS2019 <- analysisData.GRSorig %>%
select(GRS_version, GRS_reference,
ID_colnames, Celiac,
GRS) %>%
unique() %>%
left_join(ancestry_PCs, by = c("MEGA.FID", "MEGA.IID"))
analysisData.GRS2022 <- analysisData.GRSrevised %>%
select(GRS_version, GRS_reference,
ID_colnames, Celiac,
GRS) %>%
unique() %>%
left_join(ancestry_PCs, by = c("MEGA.FID", "MEGA.IID"))
analysisData.GRS2019
analysisData.GRS2022
analysisData.GRSvariants2019 <- analysisData.GRSorig %>%
select(GRS_version, GRS_reference,
ID_colnames, Celiac,
`Variant (Sharp 2019)`, Score_Allele, Dosage_for_GRS,
`Putative Gene (Sharp 2019)`) %>%
unique() %>%
left_join(ancestry_PCs, by = c("MEGA.FID", "MEGA.IID"))
analysisData.GRSvariants2022 <- analysisData.GRSrevised %>%
select(GRS_version, GRS_reference,
ID_colnames, Celiac,
`Variant (Sharp 2022)`, Score_Allele, Dosage_for_GRS,
`Putative Gene (Sharp 2019)`) %>%
unique() %>%
left_join(ancestry_PCs, by = c("MEGA.FID", "MEGA.IID"))
analysisData.GRSvariants2019
analysisData.GRSvariants2022
# Check that nrows still makes sense
analysisData.GRSvariants2019 %>% nrow()
[1] 9996
(analysisData.GRSvariants2019 %>% select(`Variant (Sharp 2019)`) %>% unique() %>% nrow())*(analysisData.GRSvariants2019 %>% select(RecordID) %>% unique() %>% nrow())
[1] 9996
analysisData.GRSvariants2022 %>% nrow()
[1] 9996
(analysisData.GRSvariants2022 %>% select(`Variant (Sharp 2022)`) %>% unique() %>% nrow())*(analysisData.GRSvariants2022 %>% select(RecordID) %>% unique() %>% nrow())
[1] 9996
analysisData.GRS2019 %>%
select(RecordID, Celiac) %>%
unique() %>%
group_by(Celiac) %>%
summarise(N = n())
analysisData.GRS2022 %>%
select(RecordID, Celiac) %>%
unique() %>%
group_by(Celiac) %>%
summarise(N = n())
analysisData.GRSvariants2019 %>%
select(RecordID, Celiac) %>%
unique() %>%
group_by(Celiac) %>%
summarise(N = n())
analysisData.GRSvariants2022 %>%
select(RecordID, Celiac) %>%
unique() %>%
group_by(Celiac) %>%
summarise(N = n())
length(unique(analysisData.GRSvariants2019$MEGA.IID))
[1] 204
length(unique(analysisData.GRSvariants2019$`Variant (Sharp 2019)`))
[1] 49
identical(nrow(analysisData.GRSvariants2019),
length(unique(analysisData.GRSvariants2019$MEGA.IID))*length(unique(analysisData.GRSvariants2019$`Variant (Sharp 2019)`)))
[1] TRUE
length(unique(analysisData.GRSvariants2022$MEGA.IID))
[1] 204
length(unique(analysisData.GRSvariants2022$`Variant (Sharp 2022)`))
[1] 49
identical(nrow(analysisData.GRSvariants2022),
length(unique(analysisData.GRSvariants2022$MEGA.IID))*length(unique(analysisData.GRSvariants2022$`Variant (Sharp 2022)`)))
[1] TRUE
Although the score weights do not change from GRS 2019 to GRS 2022, the dosage values for SNPs that were replaced are not identical. Therefore, the GRS calculated from the 2019 SNP list should be slightly different from the GRS calculated from the 2022 SNP list.
analysisData.GRS2019 %>%
select(MEGA.IID, GRS) %>%
unique() %>%
rename(GRS_2019 = GRS) %>%
full_join(analysisData.GRS2022 %>%
select(MEGA.IID, GRS) %>%
unique() %>%
rename(GRS_2022 = GRS),
by = "MEGA.IID") %>%
mutate(abs_Delta_GRS = abs(GRS_2022 - GRS_2019)) %>%
arrange(desc(abs_Delta_GRS))
# Good.
analysisData.GRS2019
analysisData.GRS2022
analysisData.GRSvariants2019
analysisData.GRSvariants2022
set.seed(1234)
fit.GRS2019 <- glm(Celiac ~ GRS,
family = binomial(link = "logit"),
data = analysisData.GRS2019)
set.seed(1234)
fit.GRS2022 <- glm(Celiac ~ GRS,
family = binomial(link = "logit"),
data = analysisData.GRS2022)
results.GRS2019 <- fit.GRS2019 %>% tidy(conf.int = TRUE) %>%
select(-c(std.error, statistic)) %>%
rename(Term = term,
logOR = estimate,
conf.low_logOR = conf.low,
conf.high_logOR = conf.high,
P = p.value) %>%
mutate(OR = exp(logOR),
conf.low_OR = exp(conf.low_logOR),
conf.high_OR = exp(conf.high_logOR)) %>%
#select(-c(logOR, conf.low_logOR, conf.high_logOR)) %>%
mutate(`95% CI` = paste("(", round(conf.low_OR, digits = 2), ", ", round(conf.high_OR, digits = 2), ")", sep = "")) %>%
mutate(OR = round(OR, digits = 2),
P = round(P, digits = 4)) %>%
filter(Term == "GRS") %>%
mutate(Term = gsub("GRS", "GRS*", Term)) %>%
select(Term, logOR, OR, `95% CI`, P)
results.GRS2022 <- fit.GRS2022 %>% tidy(conf.int = TRUE) %>%
select(-c(std.error, statistic)) %>%
rename(Term = term,
logOR = estimate, # The 'estimate' column from a logistic regression represents the logOR
conf.low_logOR = conf.low,
conf.high_logOR = conf.high,
P = p.value) %>%
mutate(OR = exp(logOR), # OR = e^OR = exp(OR)
conf.low_OR = exp(conf.low_logOR),
conf.high_OR = exp(conf.high_logOR)) %>%
#select(-c(logOR conf.low_logOR, conf.high_logOR)) %>%
mutate(`95% CI` = paste("(", round(conf.low_OR, digits = 2), ", ", round(conf.high_OR, digits = 2), ")", sep = "")) %>%
mutate(OR = round(OR, digits = 2),
P = round(P, digits = 4)) %>%
filter(Term == "GRS") %>%
mutate(Term = gsub("GRS", "GRS*", Term)) %>%
select(Term, logOR, OR, `95% CI`, P)
results.GRS2019
results.GRS2022
setwd(dir.Results)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Results inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
fwrite(results.GRS2019, "MEGA_041822_RESULTS_CDGRS2019_GRS_vs_Celiac_v0.1_JRS.csv")
fwrite(results.GRS2022, "MEGA_041822_RESULTS_CDGRS2022_GRS_vs_Celiac_v0.1_JRS.csv")
theme_set(theme_gray(base_size = 12, base_family = "Arial") +
theme(panel.border = element_rect(colour="black", fill = "transparent"),
plot.title = element_text(face="bold", hjust = 0), # lineheight=.8, size=20,
axis.text = element_text(color="black", size = 11),
axis.text.x = element_text(angle = 0, hjust = NULL),
strip.background = element_rect(colour="black", fill = "light grey", size = 1), # adjusts facet label borders (if any)
panel.background = element_blank(),
panel.grid = element_blank()
))
GrayBlue <- c("grey", "#2b8cbe")
RedBlue <- c("#CD3333", "#1874CD")
theme_set(theme_gray(base_size = 12, base_family = "Arial") +
theme(panel.border = element_rect(colour="black", fill = "transparent"),
plot.title = element_text(face="bold", hjust = 0, size = 12), # lineheight=.8, size=20,
axis.text = element_text(color="black", size = 11),
axis.text.x = element_text(angle = 0, hjust = NULL),
strip.background = element_rect(colour="black", fill = "light grey", size = 1), # adjusts facet label borders (if any)
panel.background = element_blank(),
panel.grid = element_blank()
))
analysisData.GRS2019$GRS %>% summary() # xlim(-1, 6.5)
Min. 1st Qu. Median Mean 3rd Qu. Max.
-0.653 1.016 2.055 2.437 3.894 6.490
# Min. 1st Qu. Median Mean 3rd Qu. Max.
# -0.653 1.016 2.055 2.437 3.894 6.490
analysisData.GRS2022$GRS %>% summary() # xlim(-1, 6.5)
Min. 1st Qu. Median Mean 3rd Qu. Max.
-0.653 1.016 2.050 2.449 3.966 6.490
# Min. 1st Qu. Median Mean 3rd Qu. Max.
# -0.653 1.016 2.050 2.449 3.966 6.490
analysisData.GRS2019 %>%
mutate(Group = ifelse(Celiac == 0, "DS without CD", ifelse(Celiac == 1, "DS with CD", NA)),
Group = factor(Group, levels = c("DS without CD", "DS with CD"))) %>%
ggplot(aes(x = GRS, y = ..scaled.., color = Group, fill = Group)) +
geom_density(alpha = 0.5) +
scale_colour_manual(values = GrayBlue) +
scale_fill_manual(values = GrayBlue) +
theme(legend.position = "bottom",
legend.title = element_blank(),
plot.caption = element_text(hjust = 0),
aspect.ratio = 1) +
xlab("GRS*") +
labs(title = "Celiac GRS* in DS +/- CD",
subtitle = paste("OR = ", results.GRS2019$OR[1], " ", results.GRS2019$`95% CI`[1], "\nP<", results.GRS2019$P[1], sep = ""),
caption = "*Sharp et al., 2019")
filename <- "MEGA_041822_DensityPlot_GRS2019_by_CeliacStatus_v0.1_JRS"
setwd(dir.GRSplots)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Plots inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
ggsave(filename = paste(filename, ".png", sep = ""), width = 3.6, height = 3.5, units = "in")
setwd(dir.GRSplots)
ggsave(filename = paste(filename, ".pdf", sep = ""), device = cairo_pdf, width = 3.6, height = 3.5, units = "in")
analysisData.GRS2022 %>%
mutate(Group = ifelse(Celiac == 0, "DS without CD", ifelse(Celiac == 1, "DS with CD", NA)),
Group = factor(Group, levels = c("DS without CD", "DS with CD"))) %>%
ggplot(aes(x = GRS, y = ..scaled.., color = Group, fill = Group)) +
geom_density(alpha = 0.5) +
scale_colour_manual(values = GrayBlue) +
scale_fill_manual(values = GrayBlue) +
theme(legend.position = "bottom",
legend.title = element_blank(),
plot.caption = element_text(hjust = 0),
aspect.ratio = 1) +
xlab("GRS*") +
labs(title = "Celiac GRS* in DS +/- CD",
subtitle = paste("OR = ", results.GRS2022$OR[1], " ", results.GRS2022$`95% CI`[1], "\nP<", results.GRS2022$P[1], sep = ""),
caption = "*Sharp et al., 2022")
filename <- "MEGA_041822_DensityPlot_GRS2022_by_CeliacStatus_v0.1_JRS"
setwd(dir.GRSplots)
ggsave(filename = paste(filename, ".png", sep = ""), width = 3.6, height = 3.5, units = "in")
setwd(dir.GRSplots)
ggsave(filename = paste(filename, ".pdf", sep = ""), device = cairo_pdf, width = 3.6, height = 3.5, units = "in")
# AUC from pROC::roc()
library(pROC)
Type 'citation("pROC")' for a citation.
Attaching package: ‘pROC’
The following object is masked from ‘package:sjstats’:
ci
The following objects are masked from ‘package:stats’:
cov, smooth, var
resRoc2019 <- roc(analysisData.GRS2019$Celiac ~ fit.GRS2019$fitted)
Setting levels: control = 0, case = 1
Setting direction: controls < cases
# Create a basic roc object
rocobj2019 <- roc(analysisData.GRS2019$Celiac ~ fit.GRS2019$fitted, ci = TRUE, plot=FALSE)
Setting levels: control = 0, case = 1
Setting direction: controls < cases
rocobj2019$ci # 95% CI: 0.6146-0.8517 (DeLong)
95% CI: 0.6163-0.8563 (DeLong)
ciobj2019 <- ci.se(rocobj2019, specificities=seq(0, 1, l=25))
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dat.ci2019 <- data.frame(x = as.numeric(rownames(ciobj2019)),
lower = ciobj2019[, 1],
upper = ciobj2019[, 3])
theme_set(theme_gray(base_size = 12, base_family = "Arial") +
theme(panel.border = element_rect(colour="black", fill = "transparent"),
plot.title = element_text(face="bold", hjust = 0, size = 11), # lineheight=.8, size=20,
axis.text = element_text(color="black", size = 11),
axis.text.x = element_text(angle = 0, hjust = NULL),
strip.background = element_rect(colour="black", fill = "light grey", size = 1), # adjusts facet label borders (if any)
panel.background = element_blank(),
panel.grid = element_blank()
))
g2019 <- ggroc(rocobj2019,
alpha = 0.9,
ci = TRUE,
colour = RedBlue[[1]],
#colour = GrayBlue[[2]],
#linetype = 2,
size = 1,
legacy.axes = TRUE
) +
geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color=GrayBlue[[2]]) + #, linetype="dashed")
coord_equal() +
labs(title = "Predictive accuracy of GRS* in DS",
subtitle = paste("Area under the curve: ", round(resRoc2019$auc, digits = 4), sep = ""),
caption = "Logistic: Celiac ~ GRS*\n*Sharp et al., 2019") +
theme(plot.caption = element_text(hjust = 0)) +
ylab("Sensitivity") +
xlab("1 - Specificity")
Warning: Ignoring unknown parameters: ci
g2019
filename <- "MEGA_041822_ROC_GRS2019_vs_CeliacStatus_v0.1_JRS"
setwd(dir.GRSplots)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Plots inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
ggsave(filename = paste(filename, ".png", sep = ""), width = 3.5, height = 3.5, units = "in")
setwd(dir.GRSplots)
ggsave(filename = paste(filename, ".pdf", sep = ""), device = cairo_pdf, width = 3.5, height = 3.5, units = "in")
# AUC from pROC::roc()
library(pROC)
resRoc2022 <- roc(analysisData.GRS2022$Celiac ~ fit.GRS2022$fitted)
Setting levels: control = 0, case = 1
Setting direction: controls < cases
# Create a basic roc object
rocobj2022 <- roc(analysisData.GRS2022$Celiac ~ fit.GRS2022$fitted, ci = TRUE, plot=FALSE)
Setting levels: control = 0, case = 1
Setting direction: controls < cases
rocobj2022$ci # 95% CI: 0.6146-0.8517 (DeLong)
95% CI: 0.6155-0.8553 (DeLong)
ciobj2022 <- ci.se(rocobj2022, specificities=seq(0, 1, l=25))
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dat.ci2022 <- data.frame(x = as.numeric(rownames(ciobj2022)),
lower = ciobj2022[, 1],
upper = ciobj2022[, 3])
theme_set(theme_gray(base_size = 12, base_family = "Arial") +
theme(panel.border = element_rect(colour="black", fill = "transparent"),
plot.title = element_text(face="bold", hjust = 0, size = 11), # lineheight=.8, size=20,
axis.text = element_text(color="black", size = 11),
axis.text.x = element_text(angle = 0, hjust = NULL),
strip.background = element_rect(colour="black", fill = "light grey", size = 1), # adjusts facet label borders (if any)
panel.background = element_blank(),
panel.grid = element_blank()
))
g2022 <- ggroc(rocobj2022,
alpha = 0.9,
ci = TRUE,
colour = RedBlue[[1]],
#colour = GrayBlue[[2]],
#linetype = 2,
size = 1,
legacy.axes = TRUE
) +
geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color=GrayBlue[[2]]) + #, linetype="dashed")
coord_equal() +
labs(title = "Predictive accuracy of GRS* in DS",
subtitle = paste("Area under the curve: ", round(resRoc2022$auc, digits = 4), sep = ""),
caption = "Logistic: Celiac ~ GRS*\n*Sharp et al., 2022") +
theme(plot.caption = element_text(hjust = 0)) +
ylab("Sensitivity") +
xlab("1 - Specificity")
Warning: Ignoring unknown parameters: ci
g2022
filename <- "MEGA_041822_ROC_GRS2022_vs_CeliacStatus_v0.1_JRS"
setwd(dir.GRSplots)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Plots inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
ggsave(filename = paste(filename, ".png", sep = ""), width = 3.5, height = 3.5, units = "in")
setwd(dir.GRSplots)
ggsave(filename = paste(filename, ".pdf", sep = ""), device = cairo_pdf, width = 3.5, height = 3.5, units = "in")
analysisData.GRSvariants2019.split <- analysisData.GRSvariants2019 %>%
mutate(`Variant (Sharp 2019)` = ifelse(grepl("DQ", `Variant (Sharp 2019)`)==TRUE, `Variant (Sharp 2019)`,
paste(`Variant (Sharp 2019)`, " (", Score_Allele, ")", sep = ""))) %>%
split(., .$`Variant (Sharp 2019)`)
analysisData.GRSvariants2022.split <- analysisData.GRSvariants2022 %>%
mutate(`Variant (Sharp 2022)` = ifelse(grepl("DQ", `Variant (Sharp 2022)`)==TRUE, `Variant (Sharp 2022)`,
paste(`Variant (Sharp 2022)`, " (", Score_Allele, ")", sep = ""))) %>%
split(., .$`Variant (Sharp 2022)`)
analysisData.GRSvariants2019.split %>% tail(n=2)
$`rs990171 (A)`
$`X/X ()`
analysisData.GRSvariants2022.split %>% tail(n=2)
$`rs990171 (A)`
$`X/X ()`
analysisData.GRSvariants2019.split %>% names()
[1] "DQ2.2/DQ8" "DQ2.2/X" "DQ2.5/DQ2.2" "DQ2.5/DQ8" "DQ2.5/X" "DQ7.5/DQ2.2" "DQ7.5/DQ2.5" "DQ7.5/DQ8" "DQ7.5/X"
[10] "DQ8/X" "rs10167650 (G)" "rs1018326 (C)" "rs1050976 (T)" "rs10800746 (T)" "rs10892258 (A)" "rs11851414 (C)" "rs11875687 (C)" "rs12068671 (C)"
[19] "rs12142280 (A)" "rs1250552 (G)" "rs13003464 (G)" "rs13132308 (G)" "rs1353248 (T)" "rs1359062 (C)" "rs1378938 (T)" "rs1611710 (T)" "rs17264332 (G)"
[28] "rs182429 (A)" "rs1893592 (C)" "rs1980422 (C)" "rs2030519 (G)" "rs2301226 (G)" "rs2387397 (G)" "rs2561288 (T)" "rs3128927 (T)" "rs3184504 (T)"
[37] "rs4143332 (C)" "rs4445406 (C)" "rs4821124 (C)" "rs55743914 (T)" "rs61579022 (A)" "rs61907765 (T)" "rs6498114 (G)" "rs6715106 (G)" "rs6937061 (G)"
[46] "rs7104791 (T)" "rs7616215 (C)" "rs990171 (A)" "X/X ()"
analysisData.GRSvariants2022.split %>% names()
[1] "DQ2.2/DQ8" "DQ2.2/X" "DQ2.5/DQ2.2" "DQ2.5/DQ8" "DQ2.5/X" "DQ7.5/DQ2.2" "DQ7.5/DQ2.5" "DQ7.5/DQ8" "DQ7.5/X"
[10] "DQ8/X" "rs10167650 (G)" "rs1018326 (C)" "rs1050976 (T)" "rs10800746 (T)" "rs10892258 (A)" "rs11801183 (T)" "rs11851414 (C)" "rs11875687 (C)"
[19] "rs12068671 (C)" "rs1250552 (G)" "rs13003464 (G)" "rs13132308 (G)" "rs1323292 (G)" "rs1353248 (T)" "rs1378938 (T)" "rs1611710 (T)" "rs17264332 (G)"
[28] "rs182429 (A)" "rs1893592 (C)" "rs1980422 (C)" "rs2030519 (G)" "rs2301226 (G)" "rs2561288 (T)" "rs3128927 (T)" "rs3184504 (T)" "rs4143332 (G)"
[37] "rs4445406 (C)" "rs4821124 (C)" "rs55743914 (T)" "rs61579022 (A)" "rs61907765 (T)" "rs6498114 (G)" "rs6715106 (G)" "rs6937061 (G)" "rs7104791 (T)"
[46] "rs7616215 (C)" "rs947474 (G)" "rs990171 (A)" "X/X ()"
results.variants.GRS2019 <- map2(.x = fit.variants.GRS2019,
.y = analysisData.GRSvariants2019.split,
.f = ~tidy(x = .x, conf.int=TRUE, data = .y)) %>%
bind_rows(.id="Variant") %>%
mutate(Model_Call= 'glm(Celiac ~ Dosage_for_GRS + PC1 + PC2 + PC3 + PC4 + PC5, family = binomial(link = "logit"), data = .)') %>%
select(Model_Call, everything()) %>%
filter(term == "Dosage_for_GRS") %>%
#group_by(term) %>% # Group by term if you haven't already limited your results dataframe to the variable for which you want to calculate adjusted P-values
mutate(Q = p.adjust(p.value, method = "BH")) %>%
#ungroup() %>%
mutate(GRS_version = analysisData.GRSvariants2022$GRS_version[1],
GRS_reference = analysisData.GRSvariants2022$GRS_reference[1]) %>%
select(GRS_version, GRS_reference, everything()) %>%
mutate(Variant = ifelse(Variant == "X/X ()", "X/X", Variant)) %>%
rename(logOR = estimate,
P = p.value) %>%
select(-c(std.error, statistic))
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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results.variants.GRS2022 <- map2(.x = fit.variants.GRS2022,
.y = analysisData.GRSvariants2022.split,
.f = ~tidy(x = .x, conf.int=TRUE, data = .y)) %>%
bind_rows(.id="Variant") %>%
mutate(Model_Call= 'glm(Celiac ~ Dosage_for_GRS + PC1 + PC2 + PC3 + PC4 + PC5, family = binomial(link = "logit"), data = .)') %>%
select(Model_Call, everything()) %>%
filter(term == "Dosage_for_GRS") %>%
#group_by(term) %>% # Group by term first if you haven't already limited your results dataframe to the variable for which you want to calculate adjusted P-values
mutate(Q = p.adjust(p.value, method = "BH")) %>%
#ungroup() %>%
mutate(GRS_version = analysisData.GRSvariants2022$GRS_version[1],
GRS_reference = analysisData.GRSvariants2022$GRS_reference[1]) %>%
select(GRS_version, GRS_reference, everything()) %>%
mutate(Variant = ifelse(Variant == "X/X ()", "X/X", Variant)) %>%
rename(logOR = estimate,
P = p.value) %>%
select(-c(std.error, statistic))
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results.variants.GRS2019 %>% arrange(P)
results.variants.GRS2022 %>% arrange(P)
setwd(dir.Results)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Results inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
fwrite(results.variants.GRS2019, "MEGA_041822_RESULTS_CDGRS2019_VariantDosage_vs_Celiac_v0.1_JRS.csv")
fwrite(results.variants.GRS2022, "MEGA_041822_RESULTS_CDGRS2022_VariantDosage_vs_Celiac_v0.1_JRS.csv")
# results.variants.GRS2019
# Setting and modifying theme for plots
theme_set(theme_gray(base_size = 12, base_family = "Arial") +
theme(panel.border = element_rect(colour="black", fill = "transparent"),
plot.title = element_text(face="bold", hjust = 0), # lineheight=.8, size=20,
axis.text = element_text(color="black", size = 14),
axis.text.x = element_text(angle = 0, hjust = NULL),
strip.background = element_rect(colour="black", fill = "light grey", size = 1), # adjusts facet label borders (if any)
panel.background = element_blank(),
panel.grid = element_blank()
))
#
standard_colors <- c("#333333", "#009b4e")
summary(results.variants.GRS2019$logOR)
Min. 1st Qu. Median Mean 3rd Qu. Max.
-16.21998 -0.27000 -0.03955 -0.27284 0.30717 1.76509
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#-16.193 0.000 0.000 -0.270 0.000 1.471
results.variants.GRS2019 %>%
mutate(Q.Result_Category = ifelse(Q<0.10 & logOR>0, "Significantly up in DS with CD",
ifelse(Q<0.10 & logOR<0, "Significantly down in DS with CD", "Not statistically significant")),
P.Result_Category = ifelse(P<0.10 & logOR>0, "Significantly up in DS with CD",
ifelse(P<0.10 & logOR<0, "Significantly down in DS with CD", "Not statistically significant"))) %>%
arrange(desc(abs(logOR))) %>%
mutate(rank_logOR = row_number()) %>%
arrange(P) %>%
mutate(rank_P = row_number()) %>%
mutate(label = ifelse(rank_logOR<5 | rank_P<5, Variant, "")) %>%
ggplot(aes(logOR, -log10(Q))) +
geom_hline(yintercept = -log10(0.1), linetype = 2) +
geom_vline(xintercept = 0, linetype = 2) +
#geom_point(
# aes(color = "All")
# ) +
geom_point(data = . %>% filter(Q.Result_Category=="Not statistically significant"),
aes(), color = "dark gray") +
geom_point(data = . %>% filter(Q.Result_Category=="Significantly up in DS with CD"),
aes(), colour = "#153152") +
geom_point(data = . %>% filter(Q.Result_Category=="Significantly down in DS with CD"),
aes(), colour = "#006c9e") +
xlim(-20, 20) +
ylim(0,2) +
# set colors
xlab(bquote(''~log(OR)~'')) +
ylab(bquote(''~-log[10](Q)~'')) +
#ylab(bquote('-log10'~P[BH]~)) +
scale_color_manual(values = c("Not statistically significant" = "grey",
"Significantly up in DS with CD" = "#153152",
"Significantly down in DS with CD" = "#006c9e"), name = NULL) +
# Add gene labels
geom_text_repel(aes(label = label)) + #, xlim = c(2,4)) +
theme(aspect.ratio = 1.2,
#legend.position = c(0.15, 0.9), # depends on data scales
legend.position = "none" ) +
# legend.background = element_blank() ) +
labs(title = "Variant association with Celiac in DS",
caption = results.variants.GRS2019$Model_Call[1])
Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
setwd(dir.GRSplots)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Plots inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
filename <- "MEGA_041822_VolcanoPlot_GRS2019_Celiac_vs_Dosage_adj5PCs_displayQvals_v0.1_JRS"
ggsave(filename = paste(filename, ".png", sep = ""),
width = 5, height = 5, units = "in")
Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
ggsave(filename = paste(filename, ".pdf", sep = ""),
device = cairo_pdf, width = 5, height = 5, units = "in")
Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
results.variants.GRS2019 %>%
mutate(Q.Result_Category = ifelse(Q<0.10 & logOR>0, "Significantly up in DS with CD",
ifelse(Q<0.10 & logOR<0, "Significantly down in DS with CD", "Not statistically significant")),
P.Result_Category = ifelse(P<0.10 & logOR>0, "Significantly up in DS with CD",
ifelse(P<0.10 & logOR<0, "Significantly down in DS with CD", "Not statistically significant"))) %>%
arrange(desc(abs(logOR))) %>%
mutate(rank_logOR = row_number()) %>%
arrange(P) %>%
mutate(rank_P = row_number()) %>%
mutate(label = ifelse(rank_logOR<5 | rank_P<5, Variant, "")) %>%
ggplot(aes(logOR, -log10(P))) +
geom_hline(yintercept = -log10(0.1), linetype = 2) +
geom_vline(xintercept = 0, linetype = 2) +
#geom_point(
# aes(color = "All")
# ) +
geom_point(data = . %>% filter(Q.Result_Category=="Not statistically significant"),
aes(), color = "dark gray") +
geom_point(data = . %>% filter(Q.Result_Category=="Significantly up in DS with CD"),
aes(), colour = "#153152") +
geom_point(data = . %>% filter(Q.Result_Category=="Significantly down in DS with CD"),
aes(), colour = "#006c9e") +
xlim(-20, 20) +
ylim(0,2) +
# set colors
xlab(bquote(''~log(OR)~'')) +
ylab(bquote(''~-log[10](P)~'')) +
#ylab(bquote('-log10'~P[BH]~)) +
scale_color_manual(values = c("Not statistically significant" = "grey",
"Significantly up in DS with CD" = "#153152",
"Significantly down in DS with CD" = "#006c9e"), name = NULL) +
# Add gene labels
geom_text_repel(aes(label = label)) + #, xlim = c(2,4)) +
theme(aspect.ratio = 1.2,
#legend.position = c(0.15, 0.9), # depends on data scales
legend.position = "none" ) +
# legend.background = element_blank() ) +
labs(title = "Variant association with Celiac in DS",
caption = results.variants.GRS2019$Model_Call[1])
setwd(dir.GRSplots)
filename <- "MEGA_041822_VolcanoPlot_GRS2019_Celiac_vs_Dosage_adj5PCs_displayPvals_v0.1_JRS"
ggsave(filename = paste(filename, ".png", sep = ""),
width = 5, height = 5, units = "in")
ggsave(filename = paste(filename, ".pdf", sep = ""),
device = cairo_pdf, width = 5, height = 5, units = "in")
results.variants.GRS2022 %>%
mutate(Q.Result_Category = ifelse(Q<0.10 & logOR>0, "Significantly up in DS with CD",
ifelse(Q<0.10 & logOR<0, "Significantly down in DS with CD", "Not statistically significant")),
P.Result_Category = ifelse(P<0.10 & logOR>0, "Significantly up in DS with CD",
ifelse(P<0.10 & logOR<0, "Significantly down in DS with CD", "Not statistically significant"))) %>%
arrange(desc(abs(logOR))) %>%
mutate(rank_logOR = row_number()) %>%
arrange(P) %>%
mutate(rank_P = row_number()) %>%
mutate(label = ifelse(rank_logOR<5 | rank_P<5, Variant, "")) %>%
ggplot(aes(logOR, -log10(Q))) +
geom_hline(yintercept = -log10(0.1), linetype = 2) +
geom_vline(xintercept = 0, linetype = 2) +
#geom_point(
# aes(color = "All")
# ) +
geom_point(data = . %>% filter(Q.Result_Category=="Not statistically significant"),
aes(), color = "dark gray") +
geom_point(data = . %>% filter(Q.Result_Category=="Significantly up in DS with CD"),
aes(), colour = "#153152") +
geom_point(data = . %>% filter(Q.Result_Category=="Significantly down in DS with CD"),
aes(), colour = "#006c9e") +
xlim(-20, 20) +
ylim(0,2) +
# set colors
xlab(bquote(''~log(OR)~'')) +
ylab(bquote(''~-log[10](Q)~'')) +
#ylab(bquote('-log10'~P[BH]~)) +
scale_color_manual(values = c("Not statistically significant" = "grey",
"Significantly up in DS with CD" = "#153152",
"Significantly down in DS with CD" = "#006c9e"), name = NULL) +
# Add gene labels
geom_text_repel(aes(label = label)) + #, xlim = c(2,4)) +
theme(aspect.ratio = 1.2,
#legend.position = c(0.15, 0.9), # depends on data scales
legend.position = "none" ) +
# legend.background = element_blank() ) +
labs(title = "Variant association with Celiac in DS",
caption = results.variants.GRS2022$Model_Call[1])
Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider increasing max.overlaps
setwd(dir.GRSplots)
Warning: The working directory was changed to /Users/shawjes/Dropbox/EspinosaGroup/ANALYSIS/Celiac_MultiOmics/GRS/DSMIG_Shared/Manuscript_Figure1/Plots inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
filename <- "MEGA_041822_VolcanoPlot_GRS2022_Celiac_vs_Dosage_adj5PCs_displayQvals_v0.1_JRS"
ggsave(filename = paste(filename, ".png", sep = ""),
width = 5, height = 5, units = "in")
Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
ggsave(filename = paste(filename, ".pdf", sep = ""),
device = cairo_pdf, width = 5, height = 5, units = "in")
Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
results.variants.GRS2022 %>%
mutate(Q.Result_Category = ifelse(Q<0.10 & logOR>0, "Significantly up in DS with CD",
ifelse(Q<0.10 & logOR<0, "Significantly down in DS with CD", "Not statistically significant")),
P.Result_Category = ifelse(P<0.10 & logOR>0, "Significantly up in DS with CD",
ifelse(P<0.10 & logOR<0, "Significantly down in DS with CD", "Not statistically significant"))) %>%
arrange(desc(abs(logOR))) %>%
mutate(rank_logOR = row_number()) %>%
arrange(P) %>%
mutate(rank_P = row_number()) %>%
mutate(label = ifelse(rank_logOR<5 | rank_P<5, Variant, "")) %>%
ggplot(aes(logOR, -log10(P))) +
geom_hline(yintercept = -log10(0.1), linetype = 2) +
geom_vline(xintercept = 0, linetype = 2) +
#geom_point(
# aes(color = "All")
# ) +
geom_point(data = . %>% filter(Q.Result_Category=="Not statistically significant"),
aes(), color = "dark gray") +
geom_point(data = . %>% filter(Q.Result_Category=="Significantly up in DS with CD"),
aes(), colour = "#153152") +
geom_point(data = . %>% filter(Q.Result_Category=="Significantly down in DS with CD"),
aes(), colour = "#006c9e") +
xlim(-20, 20) +
ylim(0,2) +
# set colors
xlab(bquote(''~log(OR)~'')) +
ylab(bquote(''~-log[10](P)~'')) +
#ylab(bquote('-log10'~P[BH]~)) +
scale_color_manual(values = c("Not statistically significant" = "grey",
"Significantly up in DS with CD" = "#153152",
"Significantly down in DS with CD" = "#006c9e"), name = NULL) +
# Add gene labels
geom_text_repel(aes(label = label)) + #, xlim = c(2,4)) +
theme(aspect.ratio = 1.2,
#legend.position = c(0.15, 0.9), # depends on data scales
legend.position = "none" ) +
# legend.background = element_blank() ) +
labs(title = "Variant association with Celiac in DS",
caption = results.variants.GRS2022$Model_Call[1])
setwd(dir.GRSplots)
filename <- "MEGA_041822_VolcanoPlot_GRS2022_Celiac_vs_Dosage_adj5PCs_displayPvals_v0.1_JRS"
ggsave(filename = paste(filename, ".png", sep = ""),
width = 5, height = 5, units = "in")
ggsave(filename = paste(filename, ".pdf", sep = ""),
device = cairo_pdf, width = 5, height = 5, units = "in")
setwd(dir)
Table_S2 <- read.xlsx("apt15826-sup-0001-supinfo.xlsx", sheet = "Table S2", startRow = 3) %>%
separate(`Odds.Ratio.[95%.CI]`, into = c("OR", "CI"), sep = " ", extra = "merge", remove = TRUE) %>%
rename(OR.GRS = OR,
CI.GRS = CI,
Weight.GRS = `Weight.(β)`)
Table_S2
setwd(dir)
Table_S3 <- read.xlsx("apt15826-sup-0001-supinfo.xlsx", sheet = "Table S3", startRow = 3) %>%
rename(OR.GRS = OR,
Weight.GRS = `Weight.(β)`)
Table_S3
analysisData %>%
select(RecordID, Celiac) %>%
unique() %>%
group_by(Celiac) %>%
summarise(N = n())
# Good.
analysisData.GRS <- analysisData %>%
select(-c(Variant, Dosage, MEGA.VariantID,
AT_GC_SNP, MEGA.CHR, MEGA.BP, Weight.GRS,)) %>%
unique()
analysisData.GRS
set.seed(1234)
fit.GRS <- glm(Celiac ~ GRS,
family = binomial(link = "logit"),
data = analysisData.GRS)
results.GRS <- fit.GRS %>% tidy(conf.int = TRUE) %>%
select(-c(std.error, statistic)) %>%
rename(Term = term,
logOR = estimate,
conf.low_logOR = conf.low,
conf.high_logOR = conf.high,
P = p.value) %>%
mutate(OR = exp(logOR),
conf.low_OR = exp(conf.low_logOR),
conf.high_OR = exp(conf.high_logOR)) %>%
select(-c(logOR, conf.low_logOR, conf.high_logOR)) %>%
mutate(`95% CI` = paste("(", round(conf.low_OR, digits = 2), ", ", round(conf.high_OR, digits = 2), ")", sep = "")) %>%
mutate(OR = round(OR, digits = 2),
P = round(P, digits = 4)) %>%
filter(Term == "GRS") %>%
mutate(Term = gsub("GRS", "GRS*", Term)) %>%
select(Term, OR, `95% CI`, P)
results.GRS
set.seed(1234)
fit.GRS_2components <- glm(Celiac ~ GRS.HLADQ_component + GRS.nonHLADQ_component,
family = binomial(link = "logit"),
data = analysisData.GRS)
results.GRS_2components <- fit.GRS_2components %>% tidy(conf.int = TRUE) %>%
select(-c(std.error, statistic)) %>%
rename(Term = term,
logOR = estimate,
conf.low_logOR = conf.low,
conf.high_logOR = conf.high,
P = p.value) %>%
mutate(OR = exp(logOR),
conf.low_OR = exp(conf.low_logOR),
conf.high_OR = exp(conf.high_logOR)) %>%
select(-c(logOR, conf.low_logOR, conf.high_logOR)) %>%
mutate(`95% CI` = paste("(", round(conf.low_OR, digits = 2), ", ", round(conf.high_OR, digits = 2), ")", sep = "")) %>%
mutate(OR = round(OR, digits = 2),
P = round(P, digits = 4)) %>%
filter(Term == "GRS.HLADQ_component" | Term == "GRS.nonHLADQ_component") %>%
mutate(Term = gsub("GRS.nonHLADQ_component", "GRS*, non-HLA-DQ component", Term),
Term = gsub("GRS.HLADQ_component", "GRS*, HLA-DQ component", Term)) %>%
select(Term, OR, `95% CI`, P)
results.GRS_2components
results.list <- list("GRS*" = results.GRS,
"GRS*, split components" = results.GRS_2components)
setwd(dir.Results)
write.xlsx(results.list, "Celiac_022322_RESULTS_Logistic_modifiedGRS_vs_CeliacStatus_v0.1_JRS.xlsx", overwrite=TRUE)
setwd(dir.Results)
fwrite(results.GRS, "Celiac_022322_RESULTS_Logistic_modifiedGRS_vs_CeliacStatus_v0.1_JRS.csv")
fwrite(results.GRS, "Celiac_022322_RESULTS_Logistic_modifiedGRS_vs_CeliacStatus_v0.1_JRS.tsv", sep = "\t")
setwd(dir.Results)
fwrite(results.GRS_2components, "Celiac_022322_RESULTS_Logistic_modifiedGRSsplit_vs_CeliacStatus_v0.1_JRS.csv")
fwrite(results.GRS_2components, "Celiac_022322_RESULTS_Logistic_modifiedGRSsplit_vs_CeliacStatus_v0.1_JRS.tsv", sep = "\t")
# AUC from pROC::roc()
library(pROC)
resRoc <- roc(analysisData.GRS$Celiac ~ fit.GRS_2components$fitted)
# Create a basic roc object
rocobj <- roc(analysisData.GRS$Celiac ~ fit.GRS_2components$fitted, ci = TRUE, plot=FALSE)
rocobj$ci # 95% CI: 0.6146-0.8517 (DeLong)
ciobj <- ci.se(rocobj, specificities=seq(0, 1, l=25))
dat.ci <- data.frame(x = as.numeric(rownames(ciobj)),
lower = ciobj[, 1],
upper = ciobj[, 3])
theme_set(theme_gray(base_size = 12, base_family = "Arial") +
theme(panel.border = element_rect(colour="black", fill = "transparent"),
plot.title = element_text(face="bold", hjust = 0, size = 11), # lineheight=.8, size=20,
axis.text = element_text(color="black", size = 11),
axis.text.x = element_text(angle = 0, hjust = NULL),
plot.caption = element_text(size = 8),
strip.background = element_rect(colour="black", fill = "light grey", size = 1), # adjusts facet label borders (if any)
panel.background = element_blank(),
panel.grid = element_blank()
))
g <- ggroc(rocobj,
alpha = 0.9,
ci = TRUE,
colour = RedBlue[[1]],
#colour = GrayBlue[[2]],
#linetype = 2,
size = 1,
legacy.axes = TRUE
) +
geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color=GrayBlue[[2]]) + #, linetype="dashed")
coord_equal() +
labs(title = "Predictive accuracy of GRS* in DS",
subtitle = paste("Area under the curve: ", round(resRoc$auc, digits = 4), sep = ""),
caption = "Logistic: Celiac ~ GRS_HLADQ + GRS_nonHLADQ") +
theme(plot.caption = element_text(hjust = 0)) +
ylab("Sensitivity") +
xlab("1 - Specificity")
g
filename <- "MEGA_022322_ROC_modifiedGRS_splitComponents_vs_CeliacStatus_v0.1_JRS"
setwd(dir.Figures)
ggsave(filename = paste(filename, ".png", sep = ""), width = 3.5, height = 3.5, units = "in")
setwd(dir.Figures)
ggsave(filename = paste(filename, ".pdf", sep = ""), device = cairo_pdf, width = 3.5, height = 3.5, units = "in")